1
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Polic D, Yıldırım Y, Merilaita S, Franzén M, Forsman A. Genetic structure, UV-vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies. Mol Ecol 2024; 33:e17272. [PMID: 38240162 DOI: 10.1111/mec.17272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved in the origin and dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, and for investigating whether polymorphisms represent intermediate stages of diversification towards speciation. We investigated phenotypic and genetic differentiation between two colour morphs of the butterfly Fabriciana adippe using a combination of ddRAD-sequencing and comparisons of body size, colour patterns and optical properties of bright wing spots. The silvery-spotted adippe form had larger and darker wings and reflected UV light, while the yellow cleodoxa form displayed more green scales and reflected very little UV, showcasing that they constitute distinct and alternative integrated phenotypes. Genomic analyses revealed genetic structuring according to source population, and to colour morph, suggesting that the phenotypic differentiation reflects evolutionary modifications. We report 17 outlier loci associated with colour morph, including ultraviolet-sensitive visual pigment (UVRh1), which is associated with intraspecific communication and mate choice in butterflies. Together with the demonstration that the wings of the adippe (but essentially not the cleodoxa) morph reflect UV light, that UV reflectance is higher in females than males and that morphs differ in wing size, this suggests that these colour morphs might represent genetically integrated phenotypes, possibly adapted to different microhabitats. We propose that non-random mating might contribute to the differentiation and maintenance of the polymorphism.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Sami Merilaita
- Department of Biology, University of Turku, Turku, Finland
| | - Markus Franzén
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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2
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Ivanov V, Lee KM, Mutanen M. ddRAD Sequencing and DNA Barcoding. Methods Mol Biol 2024; 2744:213-221. [PMID: 38683321 DOI: 10.1007/978-1-0716-3581-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.
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Affiliation(s)
- Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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3
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Khan M, Joshi M, Espeland M, Huemer P, Lopez-Vaamonde C, Mutanen M. Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture. Mol Ecol 2024; 33:e17194. [PMID: 37933590 DOI: 10.1111/mec.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.
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Affiliation(s)
- Maria Khan
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Hall, Austria
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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4
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Raheem DC, Gower DJ, Breugelmans K, Ranawana KB, Backeljau T. The systematics and evolution of the Sri Lankan rainforest land snail Corilla: New insights from RADseq-based phylogenetics. Mol Phylogenet Evol 2023; 182:107731. [PMID: 36781030 DOI: 10.1016/j.ympev.2023.107731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
The stylommatophoran land-snail genus Corilla is endemic to Sri Lanka and India's Western Ghats. On the basis of habitat distribution and shell morphology, the 10 extant Sri Lankan species fall into two distinct groups, lowland and montane. Here, we use phylogenetic analyses of restriction-site-associated DNA sequencing (RADseq) data and ancestral-state reconstructions of habitat association and shell morphology to clarify the systematics and evolution of Sri Lankan Corilla. Our dataset consists of 9 species of Corilla. Phylogenetic analyses were based on 88 assemblies (9,604-4,132,850 bp) generated by the RADseq assembler ipyrad, using four parameter combinations and different levels of missing data. Trees were inferred using a maximum likelihood (ML) approach. Ancestral states were reconstructed using maximum parsimony (MP) and ML approaches, with 1 binary state character analysed for habitat association (lowland vs montane) and 6 binary state characters analysed for shell morphology (shape, colour, lip width, length of upper palatal folds, orientation of upper palatal folds and collabral sculpture). Over a wide range of missing data (40-87 % missing individuals per locus) and assembly sizes (62,279-4,132,850 bp), nearly all trees conformed to one of two topologies (A and B), most relationships were strongly supported and total branch support approached the maximal value. Apart from the position of Corilla odontophora 'south', topologies A and B showed similar, well-resolved relationships at and above the species level. Our study agrees with the shell-based taxonomy of C. adamsi, C. beddomeae, C. carabinata, C. colletti and C. humberti (all maximally supported as monophyletic species). It shows that C. erronea and C. fryae constitute a single relatively widespread species (for which the valid name is C. erronea) and that the names C. gudei and C. odontophora each apply to at least two distinct, yet conchologically-cryptic species. The MP and ML ancestral-state reconstructions yielded broadly similar results and provide firm evidence that diversification in Sri Lankan Corilla has involved evolutionary convergence in the shell morphology of lowland lineages, with a pale shell and wide lip having evolved on at least two separate occasions (in C. carabinata and C. colletti) from montane ancestors having a dark, narrow-lipped shell.
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Affiliation(s)
- Dinarzarde C Raheem
- Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale 50300, Sri Lanka; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK.
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Karin Breugelmans
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Kithsiri B Ranawana
- Department of Zoology, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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5
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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6
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Ai W, Liu Y, Mei M, Zhang X, Tan E, Liu H, Han X, Zhan H, Lu X. A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica). Mol Ecol Resour 2022; 22:2396-2410. [PMID: 35377556 DOI: 10.1111/1755-0998.13616] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/13/2022] [Accepted: 03/29/2022] [Indexed: 11/26/2022]
Abstract
Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white oak species native to and widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly of Q. mongolica, a representative white oak species, by combining Illumina and PacBio data with Hi-C mapping technologies that is the first reference genome created for an Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb, with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored 774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The contig N50 and scaffold N50 were 2.64 Mb and 66.74 Mb, respectively. Of the 36,553 protein-coding genes predicted in the study, approximately 95% had functional annotations in public databases. A total of 435.34 Mb (53.75% of the genome) of repetitive sequences were predicted in the assembled genome. Genome evolution analysis showed that Q. mongolica is closely related to Q. robur from Europe, and they shared a common ancestor ~11.8 million years ago. Gene family evolution analysis of Q. mongolica revealed that the nucleotide-binding site (NBS)-encoding gene family related to disease resistance was significantly contracted, whereas the ECERIFERUM 1 (CER1) homologous genes related to cuticular wax biosynthesis was significantly expanded. This pioneering Asian oak genome resource represents an important supplement to the oak genomics community and will improve our understanding of Asian white oak biology and evolution.
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Affiliation(s)
- Wanfeng Ai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yanqun Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Mei Mei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,Biotechnology and Analysis Test Center, Liaoning Academy of Forest Science, Shenyang, 110032, Liaoning, China
| | - Xiaolin Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Enguang Tan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanzhang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiaoyi Han
- College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hao Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Xiujun Lu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.,College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
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7
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Berggren K, Aarvik L, Huemer P, Lee KM, Mutanen M. Integrative taxonomy reveals overlooked cryptic diversity in the conifer feeding Batrachedra pinicolella (Zeller, 1839) (Lepidoptera, Batrachedridae). Zookeys 2022; 1085:165-182. [PMID: 35210909 PMCID: PMC8847276 DOI: 10.3897/zookeys.1085.76853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/20/2022] [Indexed: 11/14/2022] Open
Abstract
During efforts to generate DNA barcodes for all European Lepidoptera, Batrachedrapinicolella (Zeller, 1839) was found to comprise two genetically distinct clusters. Morphological investigation and results from two nuclear markers and ddRAD sequencing furthermore support the existence of two distinct taxa which we treat as two separate species, B.pinicolella and B.confusellasp. nov. A lectotype for B.pinicolella is designated. Available data indicate that the biology of both species also differs, with Piceaabies (L.) Karsten as a proved host-plant for B.pinicolella and Pinussylvestris L. for B.confusellasp. nov. Both species are mainly distributed on the European continent with B.pinicolella occurring in boreal parts of North and Central Europe and introduced to Canada, reflecting a boreo-montane distribution pattern. Batrachedraconfusellasp. nov. is more widely distributed in temperate Northern and Central Europe.
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8
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Scalercio S, Infusino M, Huemer P, Mutanen M. Pruning the Barcode Index Numbers tree: Morphological and genetic evidence clarifies species boundaries in the
Eupithecia conterminata
complex (Lepidoptera: Geometridae) in Europe. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Stefano Scalercio
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Marco Infusino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia Agraria Centro di Ricerca Foreste e Legno Rende Italy
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H. Naturwissenschaftliche Sammlungen Hall Austria
| | - Marko Mutanen
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
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9
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How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae). Mol Phylogenet Evol 2021; 167:107342. [PMID: 34785384 DOI: 10.1016/j.ympev.2021.107342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/05/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022]
Abstract
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.
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10
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Ortiz D, Pekár S, Dianat M. Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics. Cladistics 2021; 38:320-334. [PMID: 34699083 DOI: 10.1111/cla.12493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 11/28/2022] Open
Abstract
RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
| | - Malahat Dianat
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czechia
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11
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Roslin T, Somervuo P, Pentinsaari M, Hebert PDN, Agda J, Ahlroth P, Anttonen P, Aspi J, Blagoev G, Blanco S, Chan D, Clayhills T, deWaard J, deWaard S, Elliot T, Elo R, Haapala S, Helve E, Ilmonen J, Hirvonen P, Ho C, Itämies J, Ivanov V, Jakovlev J, Juslén A, Jussila R, Kahanpää J, Kaila L, Jari-PekkaKaitila, Kakko A, Kakko I, Karhu A, Karjalainen S, Kjaerandsen J, Koskinen J, Laasonen EM, Laasonen L, Laine E, Lampila P, Levesque-Beaudin V, Lu L, Lähteenaro M, Majuri P, Malmberg S, Manjunath R, Martikainen P, Mattila J, McKeown J, Metsälä P, Miklasevskaja M, Miller M, Miskie R, Muinonen A, Veli-MattiMukkala, Naik S, Nikolova N, Nupponen K, Ovaskainen O, Österblad I, Paasivirta L, Pajunen T, Parkko P, Paukkunen J, Penttinen R, Perez K, Pohjoismäki J, Prosser S, Raekunnas M, Rahulan M, Rannisto M, Ratnasingham S, Raukko P, Rinne A, Rintala T, Miranda Romo S, Salmela J, Salokannel J, Savolainen R, Schulman L, Sihvonen P, Soliman D, Sones J, Steinke C, Ståhls G, Tabell J, Tiusanen M, Várkonyi G, Vesterinen EJ, Viitanen E, Vikberg V, Viitasaari M, Vilen J, Warne C, Wei C, Winqvist K, Zakharov E, Mutanen M. A molecular-based identification resource for the arthropods of Finland. Mol Ecol Resour 2021; 22:803-822. [PMID: 34562055 DOI: 10.1111/1755-0998.13510] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
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Affiliation(s)
- Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jireh Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Petri Ahlroth
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Perttu Anttonen
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Santiago Blanco
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dean Chan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Jeremy deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Stephanie deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Tyler Elliot
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Riikka Elo
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Jari Ilmonen
- Metsähallitus, Parks & Wildlife Finland, Vantaa, Finland
| | | | - Chris Ho
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | | | - Aino Juslén
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Jere Kahanpää
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Lauri Kaila
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | | | | | - Iiro Kakko
- Forssa Museum of Natural History, Forssa, Finland
| | | | | | - Jostein Kjaerandsen
- The Arctic University Museum of Norway, UiT -The Arctic University of Norway, Langnes, Tromsø, Norway
| | - Janne Koskinen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | | | | | | | | | | | - Liuqiong Lu
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meri Lähteenaro
- Division of Systematics, Department of Zoology, Stockholm University, Stockholm, Sweden.,Department of Entomology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Ramya Manjunath
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Jaclyn McKeown
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Meredith Miller
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Renee Miskie
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | | | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Nadia Nikolova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Timo Pajunen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Juho Paukkunen
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Ritva Penttinen
- Zoological Museum, Biodiversity Unit, University of Turku, Turku, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Kate Perez
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Sean Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Miduna Rahulan
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Meeri Rannisto
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Jukka Salmela
- Regional Museum of Lapland, Arktikum, Rovaniemi, Finland.,Arctic Centre, University of Lapland, Rovaniemi, Finland
| | | | - Riitta Savolainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Leif Schulman
- Finnish Environment Institute (SYKE), Helsinki, Finland.,Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Pasi Sihvonen
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | - Dina Soliman
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Jayme Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Claudia Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gunilla Ståhls
- Finnish Museum of Natural History 'Luomus', University of Helsinki, Helsinki, Finland
| | | | - Mikko Tiusanen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Gergely Várkonyi
- Biodiversity Centre, Finnish Environment Institute SYKE, Kuhmo, Finland
| | - Eero J Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biology, University of Turku, Turku, Finland
| | | | | | | | | | - Connor Warne
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Catherine Wei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Evgeny Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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12
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Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans. Mol Phylogenet Evol 2021; 163:107233. [PMID: 34139346 DOI: 10.1016/j.ympev.2021.107233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/25/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
Genome-level sequencing is the next step in understanding species-level relationships within Anthozoa (soft corals, anemones, stony corals, and their kin) as morphological and PCR-directed (single-locus) sequencing methods often fall short of differentiating species. The sea anemone genus Metridium is a common northern temperate sea anemone whose species are difficult to differentiate using morphology alone. Here we use Metridium as a case study to confirm the low level of information available in six loci for species differentiation commonly sequenced for Actiniaria and explore and compare the efficacy of ddRAD and sequence-capture methods in species-level systematics and biogeographic studies. We produce phylogenetic trees from concatenated datasets and perform DAPC and STRUCTURE analyses using SNP data. The six conventional loci are not able to consistently differentiate species within Metridium. The sequence-capture dataset resulted in high support and resolution for both current species and relationships between geographic areas. The ddRAD datasets displayed ambiguity among species, and support between major geographic groupings was not as high as the sequence-capture datasets. The level of resolution and support resulting from the sequence-capture data, combined with the ability to add additional individuals and expand beyond the genus Metridium over time, emphasizes the utility of sequence-capture methods for both systematics and future biogeographic studies within anthozoans. We discuss the strengths and weaknesses of the genomic approaches in light of our findings and suggest potential implications for the biogeography of Metridium based on our sampling.
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13
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Cerca J, Maurstad MF, Rochette NC, Rivera‐Colón AG, Rayamajhi N, Catchen JM, Struck TH. Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- José Cerca
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- Department of Natural History NTNU University MuseumNorwegian University of Science and Technology Trondheim Norway
| | - Marius F. Maurstad
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
- Centre for Ecological and Evolutionary Synthesis University of Oslo Oslo Norway
| | - Nicolas C. Rochette
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Angel G. Rivera‐Colón
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Niraj Rayamajhi
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐ChampaignUrbana‐Champaign IL USA
| | - Torsten H. Struck
- Frontiers in Evolutionary Zoology Natural History MuseumUniversity of Oslo Oslo Norway
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14
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Lopez-Vaamonde C, Kirichenko N, Cama A, Doorenweerd C, Godfray HCJ, Guiguet A, Gomboc S, Huemer P, Landry JF, Laštůvka A, Laštůvka Z, Lee KM, Lees DC, Mutanen M, van Nieukerken EJ, Segerer AH, Triberti P, Wieser C, Rougerie R. Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.626752] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gracillariidae is the most species-rich leaf-mining moth family with over 2,000 described species worldwide. In Europe, there are 263 valid named species recognized, many of which are difficult to identify using morphology only. Here we explore the use of DNA barcodes as a tool for identification and species discovery in European gracillariids. We present a barcode library including 6,791 COI sequences representing 242 of the 263 (92%) resident species. Our results indicate high congruence between morphology and barcodes with 91.3% (221/242) of European species forming monophyletic clades that can be identified accurately using barcodes alone. The remaining 8.7% represent cases of non-monophyly making their identification uncertain using barcodes. Species discrimination based on the Barcode Index Number system (BIN) was successful for 93% of species with 7% of species sharing BINs. We discovered as many as 21 undescribed candidate species, of which six were confirmed from an integrative approach; the other 15 require additional material and study to confirm preliminary evidence. Most of these new candidate species are found in mountainous regions of Mediterranean countries, the South-Eastern Alps and the Balkans, with nine candidate species found only on islands. In addition, 13 species were classified as deep conspecific lineages, comprising a total of 27 BINs with no intraspecific morphological differences found, and no known ecological differentiation. Double-digest restriction-site associated DNA sequencing (ddRAD) analysis showed strong mitonuclear discrepancy in four out of five species studied. This discordance is not explained by Wolbachia-mediated genetic sweeps. Finally, 26 species were classified as “unassessed species splits” containing 71 BINs and some involving geographical isolation or ecological specialization that will require further study to test whether they represent new cryptic species.
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15
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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16
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Ivanov V, Marusik Y, Pétillon J, Mutanen M. Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae). Sci Rep 2021; 11:2177. [PMID: 33500478 PMCID: PMC7838170 DOI: 10.1038/s41598-021-81788-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.
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Affiliation(s)
- Vladislav Ivanov
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Yuri Marusik
- grid.493323.c0000 0004 0399 5314Institute for Biological Problems of the North, RAS, Magadan, Russia ,grid.412219.d0000 0001 2284 638XDepartment of Zoology and Entomology, University of the Free State, Bloemfontein, 9300 South Africa
| | - Julien Pétillon
- grid.410368.80000 0001 2191 9284UMR CNRS ECOBIO, Université de Rennes 1, Rennes, France
| | - Marko Mutanen
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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17
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Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results? Mol Genet Genomics 2021; 296:457-471. [PMID: 33469716 DOI: 10.1007/s00438-020-01756-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
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18
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Gutiérrez-Rodríguez J, Zaldívar-Riverón A, Solano-Zavaleta I, Campbell JA, Meza-Lázaro RN, Flores-Villela O, Nieto-Montes de Oca A. Phylogenomics of the Mesoamerican alligator-lizard genera Abronia and Mesaspis (Anguidae: Gerrhonotinae) reveals multiple independent clades of arboreal and terrestrial species. Mol Phylogenet Evol 2020; 154:106963. [PMID: 32950681 DOI: 10.1016/j.ympev.2020.106963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/30/2020] [Accepted: 09/08/2020] [Indexed: 11/19/2022]
Abstract
Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa.
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Affiliation(s)
- Jorge Gutiérrez-Rodríguez
- Laboratorio de Herpetología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico; Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico
| | - Israel Solano-Zavaleta
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico
| | - Jonathan A Campbell
- Department of Biology, The University of Texas at Arlington, Arlington, TX, USA
| | - Rubi N Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico
| | - Oscar Flores-Villela
- Laboratorio de Herpetología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico
| | - Adrián Nieto-Montes de Oca
- Laboratorio de Herpetología, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510 Ciudad de México, Mexico.
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19
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A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01275-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Huemer P, Haxaire J, Lee KM, Mutanen M, Pekarsky O, Scalercio S, Ronkay L. Revision of the genus Hoplodrina Boursin, 1937 (Lepidoptera, Noctuidae, Xyleninae). I. Hoplodrina octogenaria (Goeze, 1781) and its sister species H. alsinides (Costantini, 1922) sp. rev. in Europe. Zookeys 2020; 927:75-97. [PMID: 32341676 PMCID: PMC7180165 DOI: 10.3897/zookeys.927.51142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/20/2020] [Indexed: 12/04/2022] Open
Abstract
The taxonomic status of the European Hoplodrinaoctogenaria (Goeze, 1781) is discussed and its partly sympatric sister species, Hoplodrinaalsinides (Costantini, 1922) sp. rev., is separated and re-described based on morphological and molecular taxonomic evidence. The adults and their genitalia are illustrated and DNA barcodes, as well as genome-wide single nucleotide polymorphism data collected by fractional genome sequencing (ddRAD), of the two species are provided.
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Affiliation(s)
- Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Krajnc-Str. 1, A-6060 Hall, Austria Tiroler Landesmuseen Betriebsges.m.b.H. Innsbruck Austria
| | - Jean Haxaire
- Le Roc, 47310 LaPlume, France Unaffiliated LaPlume France
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, FI-90014, Oulu, Finland University of Oulu Oulu Finland
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, FI-90014, Oulu, Finland University of Oulu Oulu Finland
| | - Oleg Pekarsky
- Felsőerdősor u. 16-18, H-1068, Budapest, Hungary Unaffiliated Budapest Hungary
| | - Stefano Scalercio
- Council for Agriculture Research and Economics, Research Centre for Forestry and Wood, Rende, Italy Council for Agriculture Research and Economics Rende Italy
| | - László Ronkay
- Hungarian Natural History Museum, Budapest, Hungary Hungarian Natural History Museum Budapest Hungary
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21
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Hundsdoerfer AK, Lee KM, Kitching IJ, Mutanen M. Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths. Genome Biol Evol 2020; 11:2136-2150. [PMID: 31143925 PMCID: PMC6685492 DOI: 10.1093/gbe/evz113] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of “when do nondiscrete entities become distinct, mutually exclusive evolutionary units”? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.
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Affiliation(s)
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Finland
| | - Ian J Kitching
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Finland
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22
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Lee KM, Ranta P, Saarikivi J, Kutnar L, Vreš B, Dzhus M, Mutanen M, Kvist L. Using genomic information for management planning of an endangered perennial, Viola uliginosa. Ecol Evol 2020; 10:2638-2649. [PMID: 32185008 PMCID: PMC7069310 DOI: 10.1002/ece3.6093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/17/2019] [Accepted: 01/21/2020] [Indexed: 11/11/2022] Open
Abstract
Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure, and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site-associated DNA sequencing (ddRAD-seq). We found monophyletic populations, high levels of inbreeding (mean population F SNP = 0.407-0.945), low effective population sizes (N e = 0.8-50.9), indications of past demographic expansion, and rare long-distance dispersal. Our results are important in implementing conservation strategies for V. uliginosa, which should include founding of seed banks, ex situ cultivations, and reintroductions with individuals of proper origin, combined with continuous population monitoring and habitat management.
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Affiliation(s)
- Kyung Min Lee
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Pertti Ranta
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Jarmo Saarikivi
- Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Lado Kutnar
- Department of Forest EcologySlovenian Forestry InstituteLjubljanaSlovenia
| | - Branko Vreš
- Jovan Hadži Institute of BiologyZRC SAZULjubljanaSlovenia
| | - Maxim Dzhus
- Department of BotanyBelarusian State UniversityMinskBelarus
| | - Marko Mutanen
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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Pérez-Escobar OA, Bogarín D, Schley R, Bateman RM, Gerlach G, Harpke D, Brassac J, Fernández-Mazuecos M, Dodsworth S, Hagsater E, Blanco MA, Gottschling M, Blattner FR. Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data. Mol Phylogenet Evol 2020; 144:106672. [DOI: 10.1016/j.ympev.2019.106672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023]
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25
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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26
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Prous M, Lee KM, Mutanen M. Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data. Mol Phylogenet Evol 2019; 143:106670. [PMID: 31706020 DOI: 10.1016/j.ympev.2019.106670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).
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Affiliation(s)
- Marko Prous
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Straße 90, 15374 Müncheberg, Germany; Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia.
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014, University of Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, FI-90014, University of Oulu, Finland
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27
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Martín-Hernanz S, Aparicio A, Fernández-Mazuecos M, Rubio E, Reyes-Betancort JA, Santos-Guerra A, Olangua-Corral M, Albaladejo RG. Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:1416. [PMID: 31781140 PMCID: PMC6859804 DOI: 10.3389/fpls.2019.01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/11/2019] [Indexed: 05/27/2023]
Abstract
A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.
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Affiliation(s)
- Sara Martín-Hernanz
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | - Encarnación Rubio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - J. Alfredo Reyes-Betancort
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - Arnoldo Santos-Guerra
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - María Olangua-Corral
- Departamento de Biología Reproductiva y Micro-morfología, Jardín Botánico Canario ‘Viera y Clavijo’—Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Rafael G. Albaladejo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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Dincă V, Lee KM, Vila R, Mutanen M. The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly. Proc Biol Sci 2019; 286:20191311. [PMID: 31530141 PMCID: PMC6784721 DOI: 10.1098/rspb.2019.1311] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise FST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.
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Affiliation(s)
- Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, 37, 08003 Barcelona, Spain
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, PO Box 3000, 90014 Oulu, Finland
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Coalescent-based species delimitation in the sand lizards of the Liolaemus wiegmannii complex (Squamata: Liolaemidae). Mol Phylogenet Evol 2019; 138:89-101. [DOI: 10.1016/j.ympev.2019.05.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 12/20/2022]
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30
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Rancilhac L, Goudarzi F, Gehara M, Hemami MR, Elmer KR, Vences M, Steinfarz S. Phylogeny and species delimitation of near Eastern Neurergus newts (Salamandridae) based on genome-wide RADseq data analysis. Mol Phylogenet Evol 2019; 133:189-197. [PMID: 30659915 DOI: 10.1016/j.ympev.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/01/2019] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
We reconstruct the molecular phylogeny of Near Eastern mountain brook newts of the genus Neurergus (family Salamandridae) based on newly determined RADseq data, and compare the outcomes of concatenation-based phylogenetic reconstruction with species-tree inference. Furthermore, we test the current taxonomy of Neurergus (with four species: Neurergus strauchii, N. crocatus, N. kaiseri, and N. derjugini) against coalescent-based species-delimitation approaches of our genome-wide genetic data set. While the position of N. strauchii as sister species to all other Neurergus species was consistent in all of our analyses, the phylogenetic relationships between the three remaining species changed depending on the applied method. The concatenation approach, as well as quartet-based species-tree inference, supported a topology with N. kaiseri as the closest relative to N. derjugini, while full-coalescent species-tree inference approaches supported N. crocatus as sister species of N. derjugini. Investigating the individual signal of gene trees highlighted an extensive variation among gene histories, most likely resulting from incomplete lineage sorting. Coalescent-based species-delimitation models suggest that the current taxonomy might underestimate the species richness within Neurergus and supports seven species. Based on the current sampling, our analysis suggests that N. strauchii, N. derjugini and N. kaiseri might each be subdivided into further species. However, as amphibian species are known to be composed of deep conspecific lineages that do not always warrant species status, these results need to be cautiously interpreted in an integrative taxonomic framework. We hypothesize that the rather shallow divergences detected within N. kaiseri and N. derjugini likely reflect an ongoing speciation process and thus require further investigation. On the contrary, the much deeper genetic divergence found between the two morphologically and geographically differentiated subspecies of N. strauchii leads us to propose that N. s. barani should be considered a distinct species, Neurergus barani Öz, 1994.
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Affiliation(s)
- Loïs Rancilhac
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany.
| | - Forough Goudarzi
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany; Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Marcelo Gehara
- American Museum of Natural History, Department of Herpetology, Central Park West at 79th St, New York, NY 10024, USA
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
| | - Sebastian Steinfarz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, 38106 Braunschweig, Germany
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